Re: For Sean Pitman: Some real nested hierarchies

On Mar 11, 6:26 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:

Have you read the paper? The figure 2 that you've copied onto your web
doesn't support your claim, but figure 3 blows it out of the water.

This is one of Sean's favorite techniques. If you show that he's wrong
about something, rather than reply directly to your point (or admit his
error, which would be correct), he posts a mass of irrelevant quoted
material -- as below:

Do you think Figure 3 "blows" the notion that some of the trees
produced place some groups of modern humans closer to chimps than
Neanderthals "out of the water"?

Take a look at Fig. 3:

http://mbe.oxfordjournals.org/content/vol19/issue8/images/large/mbev-19-08-04-f03.jpeg?ck=nck

Notice, in particular, the middle tree. Notice that humans are placed
closer to chimps than are Neanderthals and that "Human A" is placed
the closest.

Gutierrez comments: "In the trees drawn in figure 3 , the best score
is for the tree that joins Neandertal and chimpanzee sequences.
However, the log-likelihoods are very similar between the alternative
topologies. The Kishino-Hasegawa test (Kishino and Hasegawa 1989 )
yielded no significant differences between them at the 5% level. This
example illustrates that likelihood mapping can select as the best
topology one that is not significantly better than the other two. A
third argument against the use of likelihood mapping in this study has
to do with the database population bias mentioned earlier. It is not
advisable to perform likelihood mapping with a database where most
human sequences are very similar among themselves."

What is also interesting about these trees is that originally the
suggested range of sequence differences for modern human mtDNA went
from 1 to 24 with an average of 8 substitutions. The mtDNA sequence
differences between modern humans and the single Neanderthal fossil
range from 22 to 36 substitutions, with the average being 27. In
other words, the two most different humans analyzed in this study, as
far as mtDNA substitutions are concerned, are different by 24
substitutions. The closest that any human in this study was to the
single specimen of Neanderthal mtDNA was 22 substitutions. This means
that there are some people living today that are closer to
Neanderthals in their mtDNA sequencing than they are to some other
modern human beings. Someone might be found to be only 22
substitutions away from our Neanderthal, but 24 substitutions away
from his own next-door neighbor. Interesting isn't it? If
Neanderthals are classed as separate species because of these
differences, which one of our modern human volunteers should be
classify as a separate species? Perhaps the one who was only 22
substitutions different from the Neanderthal? Or, maybe his next-door
neighbor who is 24 substitutions away from his neighbor as well as 22
substitutions away from our Neanderthal friend? I mean, some of us
might have neighbors that look like Neanderthals (or maybe we might
look like Neanderthals compared to our neighbors), but can a different
species really be assumed based on a difference of 20-some
substitutions in a particular hypervariable region of DNA?

As it turns out, the range (1-81) for chimp/bonobo substitutions are
even wider than previously thought. In other words, if one chose a
chimp at random, this chimp might be as many as 81 substitutions
different from the chimp swinging on the branches right next to him.
This is interesting because this same chimp might be only 78
substitutions different from a given human being. This more recent
paper also points out that the range between humans (1-35) is also
wider than was reported in the first paper. The range between humans
and the Neanderthal sequence was also altered in the updated paper to
(29-43).

Krings M., Capelli C., Tschentscher F., Geisert H., Meyer S., von
Haeseler A. et al. (2000): A view of Neandertal genetic diversity.
Nature Genetics, 26:144-6.

Krings, M., Geisert, H., Schmitz, R., Krainitzki, H., and Pääbo , S.
DNA sequence of mitochondrial hypervariable region II from the
Neandertal type specimen. Evolution, Proc. Natl. Acad. Sci. USA, Vol.
96, pp. 5581-5585, May, 1999.

http://mbe.oxfordjournals.org/cgi/content/full/19/8/1359?ck=nck

Note that none of this has anything to do with some Africans being
closer to chimps than neanderthals are.

Please explain the middle tree in Figure 3 to me again . . .

http://mbe.oxfordjournals.org/content/vol19/issue8/images/large/mbev-19-08-04-f03.jpeg?ck=nck

Sean Pitman
www.DetectingDesign.com

.

Relevant Pages

  • Re: For Sean Pitman: Some real nested hierarchies
    ... closer to chimps than are Neanderthals and that "Human A" is placed ... It tells us how much sequence difference there is. ... range from 22 to 36 substitutions, ...
    (talk.origins)
  • Re: For Sean Pitman: Some real nested hierarchies
    ... The sequence is 1002 bases long, ... bonobo sequence and has a different species of gibbon from tas2r38. ... between the two groups of modern humans and the Neanderthals. ... and the single Neanderthal fossil range from 22 to 36 substitutions, ...
    (talk.origins)
  • Re: For Sean Pitman: Some real nested hierarchies
    ... closer to chimps than are Neanderthals and that "Human A" is placed ... humans have a bit less distance to the chimp; ... range from 22 to 36 substitutions, ...
    (talk.origins)
  • Re: For Sean Pitman: Some real nested hierarchies
    ... closer to chimps than are Neanderthals and that "Human A" is placed ... range from 22 to 36 substitutions, ...
    (talk.origins)
  • Re: For Sean Pitman: Some real nested hierarchies
    ... It tells us how much sequence difference there is. ... neanderthals arose as a later offshoot from one of two still extant ... branches of fully modern Homo sapiens, ... chimps" than the other group. ...
    (talk.origins)
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